Render settings questions

Currently I'm working on finishing post-production of my short stop-motion film (a lot of green screen shots). And I have some questions about codecs and such. I've been searching on the internet what the perfect settings are for exports for vimeo and film festivals and such. But I always end up more confused than I already was, and severely doubting which settings I should use. I also tried out a lot of settings, but it's all still pretty hazy for me.
So I have a couple of questions for you pro's out there!

I composite all my shots (jpg sequences) in After Effects (CS5.5) and export the final shots to Final Cut 7 for the final edit. All the shots are exported from AE with the Animation codec.

But lately I hear people saying that it's better to export the raw shots to Apple Pro Res (4444?), or a png sequence. I don't really prefer the latter, since FCP7 tends to screw up the sorting order of image sequences. And I understand that the Gamma Correction option for Pro Res can screw up your files with a lot of flickering, so it's best to leave this off? I don't want the codec to screw with my colours too much.

Also, does it matter much if the exported material is set to Premultiplied or Straight when I don't have to do compositing on the shots anymore, no screwing around with layers but just editing in FCP? Since I already did that in After Effects. Maybe I need to do some correcting on the Exposure or Levels of some shots, but thats it. I just want to make sure that I can export my raw files with the best quality.

And if I export from AE to FCP 7, does it matter if I enable "Match Legacy After Effects Quicktime Gamma Adjustments" in the project settings? It's not really clear for me if this only applies to the files when they're opened in Quicktime. Or if it also has any effect on the colors in FCP 7 or any other editing programs. And if it's the best option to enable when you render the raw shots to quicktime files.

Now the final question, about the sequence settings in FCP7. As I understand you have to match the sequence settings with the settings of the movie files you're editing. But what if you want to export the sequence to H264 or MP4 when your sequence settings are set to Animation or Pro Res? Does it matter much? Should the sequence settings be set to the same settings as your export?
I think I noticed a slight difference in color when I exported h264 files with sequence settings to Animation, and the same shot also to h264, but with a different codec set in the sequence settings. But I'm not really sure, maybe it's my imagination.

I hope someone can clear this up for me, I'm not a native english speaker, so for some questions it's a bit hard to google for me. Usually I end up reading forums and articles for hours and hours, but not getting the answers to my questions. I know a lot of the basic stuff, but I keep having lot's of doubts on specific things like the best codec to use.

[AD Narayan]"Export from FCP at sequence settings. Use MPEG Streamclip or other compression program to change into file type of choice."

But what should my sequence settings be when I export the master file, the same settings as the footage that sequence contains? And what is the best codec to render my master (from which I'll make the different renders) to, Apple Pro Res?

Woops, sorry I meant Quicktime with Animation Codec. Walter's suggestion for ProRes probably a better one though if you're cutting in FCP.

Your sequence settings should be the same as the footage the sequence contains for best results. ProRes is a good format to have your masters in. All of our FCP cut masters in our suite are stored as ProRes 422 HQ.

[Kasper Werther]"I composite all my shots (jpg sequences) in After Effects (CS5.5) and export the final shots to Final Cut 7 for the final edit. All the shots are exported from AE with the Animation codec. But lately I hear people saying that it's better to export the raw shots to Apple Pro Res (4444?), or a png sequence. I don't really prefer the latter, since FCP7 tends to screw up the sorting order of image sequences."

If you are not exporting an alpha channel for transparency, you can use ProRes 422. You will not need to change of the codec settings from their defaults.

[Kasper Werther]"Now the final question, about the sequence settings in FCP7. As I understand you have to match the sequence settings with the settings of the movie files you're editing. But what if you want to export the sequence to H264 or MP4 when your sequence settings are set to Animation or Pro Res? Does it matter much? Should the sequence settings be set to the same settings as your export? I think I noticed a slight difference in color when I exported h264 files with sequence settings to Animation, and the same shot also to h264, but with a different codec set in the sequence settings. But I'm not really sure, maybe it's my imagination."

Actually, rendering Animation codec requires you to manually set the gamma in FCP, as FCP frequently misinterprets gamma for RGB codecs like Animation. Rendering to ProRes will not require this.

I have After Effects CS4 and have been using the Animation codec to export for online videos with no problem.

My composite file is 1280 x 720. I have been using Final Cut 7.
I now need to place this (center in the middle of the frame is fine) in a 1920 x 1080 ProRes 422 file for Final Cut 10.

I have been trying to export directly from After Effects to ProRes 422 at the orginal size and at the new size and get error messages (8973) (44:39) and (44:46) when I attempt to change the export codec.

Is there a workflow solution from the Animation Codec to ProRes 422 using either: Final Cut 7, Quicktime Pro 7, or Compressor?
Please suggest the best solution?